[Bioperl-l] problem with bioperl-ext

[Tom Keller]

Been struggling to get the bioperl-ext modules to install. I've got the staden libraries:
$ ll /usr/local/lib/ | grep read
-rwxr-xr-x   1 root  wheel   265K Apr  9 11:19 libstaden-read.1.1.0.dylib
lrwxr-xr-x   1 root  wheel    26B Apr  9 11:19 libstaden-read.1.dylib -> libstaden-read.1.1.0.dylib
-rw-r--r--   1 root  wheel   810K Apr  9 11:19 libstaden-read.a
lrwxr-xr-x   1 root  wheel    26B Apr  9 11:19 libstaden-read.dylib -> libstaden-read.1.1.0.dylib
-rwxr-xr-x   1 root  wheel   886B Apr  9 11:19 libstaden-read.la

Here are the test results:
$ sudo make test
PERL_DL_NONLAZY=1 /opt/local/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/basic.t .. ok
All tests successful.
Files=1, Tests=1,  0 wallclock secs ( 0.01 usr +  0.01 sys =  0.02 CPU)
Result: PASS
PERL_DL_NONLAZY=1 /opt/local/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl<http://test.pl>
1..2
ok 1

2..2
Testing bp_sw with a protein alignment...

ProteinSW Matrix calculation: [      0] Cells  0%
one         1        WLGQRNLVSSTGGNLLNVWLKDW
                     W+G RN+V     NLLNVW +DW
two         1        WMGNRNVV-----NLLNVWFRDW


ok 2
PERL_DL_NONLAZY=1 /opt/local/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, '../blib/lib', '../blib/arch')" test.pl<http://test.pl>
test.pl<http://test.pl> .. Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read'

Can't load '/Users/kellert/Downloads/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Users/kellert/Downloads/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bundle, 2): Symbol not found: _fread_reading
  Referenced from: /Users/kellert/Downloads/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bundle
  Expected in: flat namespace
 in /Users/kellert/Downloads/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bundle at /System/Library/Perl/5.10.0/darwin-thread-multi-2level/DynaLoader.pm line 207, <DATA> line 1.
 at /Library/Perl/5.10.0/Inline.pm line 527


 at test.pl<http://test.pl> line 0
INIT failed--call queue aborted, <DATA> line 1.
test.pl<http://test.pl> .. Dubious, test returned 2 (wstat 512, 0x200)
Failed 94/94 subtests

Test Summary Report
-------------------
test.pl<http://test.pl> (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 94 tests but ran 0.
Files=1, Tests=0,  0 wallclock secs ( 0.01 usr  0.01 sys +  0.09 cusr  0.02 csys =  0.13 CPU)
Result: FAIL
Failed 1/1 test programs. 0/0 subtests failed.
make[1]: *** [test_dynamic] Error 2
make: *** [subdirs-test] Error 2


I'm running OS X 10.6.3, the rest of Bioperl is 1.6.
Suggestions greatly appreciated.

Tom
kellert at ohsu.edu<mailto:kellert at ohsu.edu>
503-494-2442